Strain identifier

BacDive ID: 5190

Type strain: Yes

Species: Xenorhabdus szentirmaii

Strain Designation: Rar

Strain history: CIP <- 2005, DSMZ <- K. Lengyel, E.L. Univ., Budapest, Hungary <- A. Fodor, E.L. Univ., Budapest, Hungary

NCBI tax ID(s): 1427518 (strain), 290112 (species)

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General

@ref: 6395

BacDive-ID: 5190

DSM-Number: 16338

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile, animal pathogen

description: Xenorhabdus szentirmaii Rar is an obligate aerobe, mesophilic, motile animal pathogen that was isolated from nematode Steinernema rarum.

NCBI tax id

NCBI tax idMatching level
290112species
1427518strain

strain history

@refhistory
6395<- K. Lengyel; Rar <- A. Fodor, Univ. Budapest
123403CIP <- 2005, DSMZ <- K. Lengyel, E.L. Univ., Budapest, Hungary <- A. Fodor, E.L. Univ., Budapest, Hungary

doi: 10.13145/bacdive5190.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Morganellaceae
  • genus: Xenorhabdus
  • species: Xenorhabdus szentirmaii
  • full scientific name: Xenorhabdus szentirmaii Lengyel et al. 2005

@ref: 6395

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus szentirmaii

full scientific name: Xenorhabdus szentirmaii Lengyel et al. 2005

strain designation: Rar

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.294
6948099.971negative
123403yesnegativerod-shaped

colony morphology

  • @ref: 123403

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6395CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
38361MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123403CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6395positivegrowth30mesophilic
38361positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123403
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.661

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68369malate+assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate+assimilation24265
68369maltose+assimilation17306
68369N-acetylglucosamine+assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose+assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose+assimilation17634
68369gelatin+hydrolysis5291
68369esculin+hydrolysis4853
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
123403nitrate-reduction17632
123403nitrite-reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12340335581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
123403oxidase-
123403alcohol dehydrogenase-1.1.1.1
123403catalase-1.11.1.6
123403lysine decarboxylase-4.1.1.18
123403ornithine decarboxylase-4.1.1.17
123403urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123403-+++-+--+-++---+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6395---+/-+/-++-+-+-+++--++-+/-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123403+/----+/------+/-+/-+/---------+/---+/-+/-+/-+/----+/---------------+/---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
6395nematode Steinernema rarumSteinernema rarumCordobaArgentinaARGMiddle and South America
123403Other, Nematode Steinernema rarumCordobaArgentinaARGMiddle and South America

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Nematoda

taxonmaps

  • @ref: 69479
  • File name: preview.99_2240.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_27;97_494;98_566;99_2240&stattab=map
  • Last taxonomy: Xenorhabdus szentirmaii
  • 16S sequence: AJ810295
  • Sequence Identity:
  • Total samples: 111
  • soil counts: 4
  • aquatic counts: 13
  • animal counts: 90
  • plant counts: 4

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
6395yes1Risk group (German classification)
1234031Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Xenorhabdus szentirmaii partial 16S rRNA gene, type strain DSM 16338T
  • accession: AJ810295
  • length: 1524
  • database: ena
  • NCBI tax ID: 290112

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus szentirmaii DSM 16338GCA_002632585scaffoldncbi1427518
66792Xenorhabdus szentirmaii DSM 16338GCA_000531455contigncbi1427518
66792Xenorhabdus szentirmaii DSM 163381427518.3wgspatric1427518
66792Xenorhabdus szentirmaii DSM 163381427518.5wgspatric1427518
66792Xenorhabdus szentirmaii DSM 163382597490185draftimg1427518

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes50.522no
gram-positiveno97.846no
anaerobicno98.61no
aerobicyes86.586no
halophileno84.09no
spore-formingno94.288no
thermophileno98.033yes
glucose-utilyes92.246yes
motileyes86.615no
glucose-fermentyes79.383yes

External links

@ref: 6395

culture collection no.: DSM 16338, CIP 108895, NCIMB 14019

straininfo link

  • @ref: 74682
  • straininfo: 132357

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15830803Description of four novel species of Xenorhabdus, family Enterobacteriaceae: Xenorhabdus budapestensis sp. nov., Xenorhabdus ehlersii sp. nov., Xenorhabdus innexi sp. nov., and Xenorhabdus szentirmaii sp. nov.Lengyel K, Lang E, Fodor A, Szallas E, Schumann P, Stackebrandt ESyst Appl Microbiol10.1016/j.syapm.2004.10.0042005Animals, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Enterobacteriaceae/classification, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhabditida/*microbiology, Ribotyping, Sequence Analysis, DNA, Species Specificity, Symbiosis, Xenorhabdus/*classification/genetics/metabolism/physiologyGenetics
21941889Szentiamide, an N-formylated cyclic depsipeptide from Xenorhabdus szentirmaii DSM 16338T.Ohlendorf B, Simon S, Wiese J, Imhoff JFNat Prod Commun2011Depsipeptides/*chemistry, Molecular Structure, Repressor Proteins, Xenorhabdus/*chemistry
Genetics24625876Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus szentirmaii Strain DSM16338.Gualtieri M, Ogier JC, Pages S, Givaudan A, Gaudriault SGenome Announc10.1128/genomeA.00190-142014
Phylogeny34898417Xenorhabdus lircayensis sp. nov., the symbiotic bacterium associated with the entomopathogenic nematode Steinernema unicornum.Castaneda-Alvarez C, Prodan S, Zamorano A, San-Blas E, Aballay EInt J Syst Evol Microbiol10.1099/ijsem.0.0051512021Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhabditida/microbiology, Sequence Analysis, DNA, *Xenorhabdus/classification/isolation & purificationTranscriptome
35335666Type Strains of Entomopathogenic Nematode-Symbiotic Bacterium Species, Xenorhabdus szentirmaii (EMC) and X. budapestensis (EMA), Are Exceptional Sources of Non-Ribosomal Templated, Large-Target-Spectral, Thermotolerant-Antimicrobial Peptides (by Both), and Iodinin (by EMC).Fodor A, Gualtieri M, Zeller M, Tarasco E, Klein MG, Fodor AM, Haynes L, Lengyel K, Forst SA, Furgani GM, Karaffa L, Vellai TPathogens10.3390/pathogens110303422022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6395Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16338)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16338
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
38361Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6576
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74682Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132357.1StrainInfo: A central database for resolving microbial strain identifiers
123403Curators of the CIPCollection of Institut Pasteur (CIP 108895)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108895